importing packages

library("devtools")
Loading required package: usethis
install_github("jw156605/SLICER")
Skipping install of 'SLICER' from a github remote, the SHA1 (cb1be8ac) has not changed since last install.
  Use `force = TRUE` to force installation
library(Seurat)
Attaching SeuratObject
library(readr)
library(tidyverse)
Registered S3 methods overwritten by 'dbplyr':
  method         from
  print.tbl_lazy     
  print.tbl_sql      
── Attaching packages ─────────────────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.0      ✔ dplyr   1.0.10
✔ tibble  3.1.8      ✔ stringr 1.5.0 
✔ tidyr   1.2.1      ✔ forcats 0.5.2 
✔ purrr   0.3.5      
── Conflicts ────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
library(HGC) 
library(latticeExtra)
Loading required package: lattice

Attaching package: ‘latticeExtra’

The following object is masked from ‘package:ggplot2’:

    layer
library(lattice) 
library(RColorBrewer)
library(clusterProfiler)
clusterProfiler v4.4.4  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

If you use clusterProfiler in published research, please cite:
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141

Attaching package: ‘clusterProfiler’

The following object is masked from ‘package:lattice’:

    dotplot

The following object is masked from ‘package:purrr’:

    simplify

The following object is masked from ‘package:stats’:

    filter
library(org.Mm.eg.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object is masked _by_ ‘.GlobalEnv’:

    normalize

The following objects are masked from ‘package:dplyr’:

    combine, intersect, setdiff, union

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff,
    sort, table, tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To
    cite Bioconductor, see 'citation("Biobase")', and for packages
    'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:clusterProfiler’:

    rename

The following objects are masked from ‘package:dplyr’:

    first, rename

The following object is masked from ‘package:tidyr’:

    expand

The following objects are masked from ‘package:base’:

    expand.grid, I, unname


Attaching package: ‘IRanges’

The following object is masked from ‘package:clusterProfiler’:

    slice

The following objects are masked from ‘package:dplyr’:

    collapse, desc, slice

The following object is masked from ‘package:purrr’:

    reduce


Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:clusterProfiler’:

    select

The following object is masked from ‘package:dplyr’:

    select
library(AnnotationDbi)

reading in normalized data again

exp = read_csv("normalized_data.csv")
New names:
• `` -> `...1`
• `` -> `...151`
• `` -> `...240`
• `` -> `...289`
• `` -> `...352`
• `` -> `...391`
• `` -> `...394`
• `` -> `...450`
• `` -> `...462`
Rows: 14414 Columns: 463
── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr   (1): ...1
dbl (454): M1_A01, M1_A02, M1_A03, M1_A05, M1_A06, M1_A08, M1_A09, M1_A10, M1_B01, M1_B03, M1_B04, M1_B05, M1_B06, ...
lgl   (8): ...151, ...240, ...289, ...352, ...391, ...394, ...450, ...462

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
exp = discard(exp,~all(is.na(.) |.  == ""))
exp = distinct(exp, `...1`, .keep_all = TRUE)
# filtering out the reprogramming transcription factors 
exp = filter(exp, !`...1`%in% c("Mef2c", "Gata4", "Tbx5"))
exp = column_to_rownames(exp, var="...1")

creating a seurat object with all of the cells


seurat.obj = CreateSeuratObject(counts = exp)
seurat.obj = NormalizeData(seurat.obj)
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
seurat.obj = FindVariableFeatures(seurat.obj, selection.method =  "vst", nfeatures = 10000)
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
all.genes = rownames(seurat.obj)
seurat.obj = ScaleData(seurat.obj, features = all.genes)
Centering and scaling data matrix

  |                                                                                        
  |                                                                                  |   0%
  |                                                                                        
  |=====                                                                             |   7%
  |                                                                                        
  |===========                                                                       |  13%
  |                                                                                        
  |================                                                                  |  20%
  |                                                                                        
  |======================                                                            |  27%
  |                                                                                        
  |===========================                                                       |  33%
  |                                                                                        
  |=================================                                                 |  40%
  |                                                                                        
  |======================================                                            |  47%
  |                                                                                        
  |============================================                                      |  53%
  |                                                                                        
  |=================================================                                 |  60%
  |                                                                                        
  |=======================================================                           |  67%
  |                                                                                        
  |============================================================                      |  73%
  |                                                                                        
  |==================================================================                |  80%
  |                                                                                        
  |=======================================================================           |  87%
  |                                                                                        
  |=============================================================================     |  93%
  |                                                                                        
  |==================================================================================| 100%
seurat.obj = RunPCA(seurat.obj, features =  VariableFeatures(seurat.obj))
PC_ 1 
Positive:  Ehd4, Acaa2, Dsp, Ldhb, Nid2, Ryr2, Myl4, Epb4.1, Smpx, Tnni3 
       Ttn, Tnnt2, Mgst3, Sort1, Ldb3, Jup, Mlf1, Baiap2l1, Rrad, Mgrn1 
       Fryl, Ppp1r3c, Fam134b, Fabp3, Cenpa, Usp28, Clu, Pcyt1a, Ddit4l, Cd24a 
Negative:  Fstl1, Bgn, Cd200, Col3a1, Rbp1, Tagln2, Fam198b, Postn, Col1a2, Tagln 
       Fbln2, Rbms3, Lox, Fbn1, Loxl1, Dhrs3, Marcks, Col8a1, 11-Sep, Col5a2 
       Clca1, Lrrc8a, Spry2, Anxa1, Ogn, Nars, Gstm2, Fbln5, Asns, Acta2 
PC_ 2 
Positive:  Top2a, Prc1, Smc2, Ccnb1, Birc5, Cdk1, Ube2c, Rrm2, Mki67, Pbk 
       Ckap2l, Asf1b, Cks2, Tpx2, Cdca8, Kif20b, 2810417H13Rik, Cks1b, Anln, Tacc3 
       Spc25, Hmmr, Hmgb2, Shcbp1, Ndc80, Mad2l1, Nuf2, Cenpe, Ect2, Cdca2 
Negative:  Cst3, B2m, Sptbn1, Malat1, Ypel5, Itm2b, Gyg, Parp3, Tspyl1, Serpine2 
       Lama2, Igfbp7, Ogn, B4galt1, Gpx3, Ctsa, Asah1, Pdcd4, Itgb5, Fhl2 
       Pam, Col4a2, Lhfp, Tcn2, Mxra8, Smim14, Ctsd, Akap13, Prex2, Impact 
PC_ 3 
Positive:  Cst3, Col4a1, Flna, Igfbp7, Col1a1, Col4a2, Myl9, Sorbs2, Fhl2, Itgb1 
       Tns1, Col14a1, Ankrd1, Tpm2, Lbh, Pcolce, Tuba1a, Postn, Tuba1b, Itga1 
       Col5a1, Actn4, Pdlim2, Myom1, Pdgfrb, Tbx20, Sorbs1, Acta2, Pcdh18, Macf1 
Negative:  Gpm6a, Mgst1, Hpgd, Gsta4, Ptgs1, Upk1b, Pkhd1l1, F11r, Msln, Bst1 
       Maf, Ezr, Mpzl2, Cxadr, Krt8, Cd55, Igfbp6, Igfbp4, Acsl4, Bex4 
       Gcnt1, Vnn1, Ftl1, Efna5, Slpi, Ptp4a2, Tmem108, Tmem154, Csde1, Bnc1 
PC_ 4 
Positive:  S100a6, Tpm1, Tpm4, Actb, Nme1, Zyx, Lgals1, Tpm2, Cryab, Actg1 
       Wisp1, Gapdh, Gm12070, Actn1, Timp1, Slc25a5, Sec13, Eif5a, Psat1, Creb3l1 
       Tnfrsf12a, Ccnd2, Csf1, Pkm, Pcolce, Acta2, Des, Rcn3, Col1a1, Wdr1 
Negative:  Egfl7, Ctla2a, Gja4, Emcn, Cdh5, Notch1, Klhl4, Gimap6, Pecam1, Stab1 
       Gpr116, Lyl1, Tie1, Entpd1, Ctla2b, Fli1, Myct1, Sox7, Thsd1, Eltd1 
       Gngt2, Mmrn2, S1pr1, Mecom, Tgfbi, Klhl24, Tmem2, Apoe, Plxnd1, Akap13 
PC_ 5 
Positive:  Egfl7, Notch1, Klhl4, Stab1, Cdh5, Emcn, Cgnl1, Pecam1, Gja4, Ramp2 
       Lyl1, Col4a1, Gpr116, Tie1, Entpd1, Zfp69, Loxl2, Eltd1, Plxnd1, Thsd1 
       Cxcl16, Col5a1, Tek, S1pr1, Txndc5, Tgfbi, Odc1, Eng, Sox7, Myct1 
Negative:  Spcs3, Impact, Ypel5, Cpne8, Lnp, Arhgap44, Sptbn1, Myo10, Nexn, Arid5b 
       Arl5a, Braf, Klhl9, Cpne3, Lama2, Mrfap1, Serping1, Mlf1, Zdhhc2, Mier3 
       Gm2a, Dstn, Emc2, Myoz2, Ncam1, Rhobtb3, Cryab, Gucy1a3, Ttn, Idh1 
ElbowPlot(seurat.obj)

Seurat clustering the entire graph to see what clusters are identified

seurat.obj = FindNeighbors(seurat.obj, dims = 1:15)
Computing nearest neighbor graph
Computing SNN
seurat.obj = FindClusters(seurat.obj, resolution = 1.75)
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 454
Number of edges: 16805

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.4797
Number of communities: 8
Elapsed time: 0 seconds

importing the results from the paper and our hierarchical clustering results for further comparison

identified_cells = read.csv("paper_cell_states.csv", row.names = 1, header=TRUE)
identified_cells = identified_cells[match(rownames(seurat.obj@meta.data), rownames(identified_cells)),]
seurat.obj@meta.data$cc_paper = identified_cells$CC
seurat.obj@meta.data$cat_paper = identified_cells$stage
seurat.obj@meta.data$cc_hclust = "CCI"
seurat.obj@meta.data[active_cells,]$cc_hclust = "CCA"
Idents(seurat.obj)  = "RNA_snn_res.1.75"

running UMAP dimensional reduction on the data to plot the data

seurat.obj = RunUMAP(seurat.obj, dims = 1:15)
Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session
00:34:45 UMAP embedding parameters a = 0.9922 b = 1.112
00:34:45 Read 454 rows and found 15 numeric columns
00:34:45 Using Annoy for neighbor search, n_neighbors = 30
00:34:45 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:34:45 Writing NN index file to temp file /var/folders/fj/09brpj8s5mz1c5wxktl80s080000gn/T//RtmpXaF6CV/fileec356c43b603
00:34:45 Searching Annoy index using 1 thread, search_k = 3000
00:34:45 Annoy recall = 100%
00:34:46 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
00:34:47 Initializing from normalized Laplacian + noise (using irlba)
00:34:47 Commencing optimization for 500 epochs, with 17028 positive edges
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
00:34:48 Optimization finished

seeing what tsne reduction makes the data do

seurat.obj = RunTSNE(seurat.obj, dims = 1:15)
DimPlot(seurat.obj, reduction = "tsne", group.by = 'RNA_snn_res.1.75')

finding differentially expressed markers in these clusters

markers = FindAllMarkers(seurat.obj, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
Calculating cluster 0

 Completed [=>---------------------------------------------------------------------------------]   2% with 0 failures
 Completed [=>---------------------------------------------------------------------------------]   3% with 0 failures
 Completed [==>--------------------------------------------------------------------------------]   3% with 0 failures
 Completed [==>--------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [============================>------------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [========================================================================>----------]  89% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [=>---------------------------------------------------------------------------------]   3% with 0 failures
 Completed [==>--------------------------------------------------------------------------------]   3% with 0 failures
 Completed [==>--------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [============================>------------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [========================================================================>----------]  89% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Calculating cluster 1

 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [===================================================================>---------------]  83% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [===================================================================>---------------]  83% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Calculating cluster 2

 Completed [===>-------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [============================>------------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [==============================================================>--------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [===================================================================>---------------]  83% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [========================================================================>----------]  89% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [===>-------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [============================>------------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [==============================================================>--------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [===================================================================>---------------]  83% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [========================================================================>----------]  89% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Calculating cluster 3

 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [========================================================================>----------]  89% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [========================================================================>----------]  89% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Calculating cluster 4

 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [============================>------------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [============================>------------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Calculating cluster 5

 Completed [==>--------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [===================================================================>---------------]  83% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [========================================================================>----------]  89% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [===>-------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [===================================================================>---------------]  83% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [========================================================================>----------]  89% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Calculating cluster 6

 Completed [=>---------------------------------------------------------------------------------]   3% with 0 failures
 Completed [==>--------------------------------------------------------------------------------]   3% with 0 failures
 Completed [==>--------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [============================>------------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [==============================================================>--------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [===================================================================>---------------]  83% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [========================================================================>----------]  89% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [=>---------------------------------------------------------------------------------]   3% with 0 failures
 Completed [==>--------------------------------------------------------------------------------]   3% with 0 failures
 Completed [==>--------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [============================>------------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [==============================================================>--------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [===================================================================>---------------]  83% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [========================================================================>----------]  89% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Calculating cluster 7

 Completed [>----------------------------------------------------------------------------------]   2% with 0 failures
 Completed [=>---------------------------------------------------------------------------------]   2% with 0 failures
 Completed [=>---------------------------------------------------------------------------------]   3% with 0 failures
 Completed [==>--------------------------------------------------------------------------------]   3% with 0 failures
 Completed [==>--------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [============================>------------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [===================================================================>---------------]  83% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [========================================================================>----------]  89% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [>----------------------------------------------------------------------------------]   2% with 0 failures
 Completed [=>---------------------------------------------------------------------------------]   2% with 0 failures
 Completed [=>---------------------------------------------------------------------------------]   3% with 0 failures
 Completed [==>--------------------------------------------------------------------------------]   3% with 0 failures
 Completed [==>--------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   4% with 0 failures
 Completed [===>-------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   5% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   6% with 0 failures
 Completed [====>------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   7% with 0 failures
 Completed [=====>-----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   8% with 0 failures
 Completed [======>----------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]   9% with 0 failures
 Completed [=======>---------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  10% with 0 failures
 Completed [========>--------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  11% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  12% with 0 failures
 Completed [=========>-------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  13% with 0 failures
 Completed [==========>------------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  14% with 0 failures
 Completed [===========>-----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  15% with 0 failures
 Completed [============>----------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  16% with 0 failures
 Completed [=============>---------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  17% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  18% with 0 failures
 Completed [==============>--------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  19% with 0 failures
 Completed [===============>-------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  20% with 0 failures
 Completed [================>------------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  21% with 0 failures
 Completed [=================>-----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  22% with 0 failures
 Completed [==================>----------------------------------------------------------------]  23% with 0 failures
 Completed [===================>---------------------------------------------------------------]  24% with 0 failures
 Completed [===================>---------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  25% with 0 failures
 Completed [====================>--------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  26% with 0 failures
 Completed [=====================>-------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  27% with 0 failures
 Completed [======================>------------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  28% with 0 failures
 Completed [=======================>-----------------------------------------------------------]  29% with 0 failures
 Completed [========================>----------------------------------------------------------]  30% with 0 failures
 Completed [========================>----------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  31% with 0 failures
 Completed [=========================>---------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  32% with 0 failures
 Completed [==========================>--------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  33% with 0 failures
 Completed [===========================>-------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  34% with 0 failures
 Completed [============================>------------------------------------------------------]  35% with 0 failures
 Completed [============================>------------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  36% with 0 failures
 Completed [=============================>-----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  37% with 0 failures
 Completed [==============================>----------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  38% with 0 failures
 Completed [===============================>---------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  39% with 0 failures
 Completed [================================>--------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  40% with 0 failures
 Completed [=================================>-------------------------------------------------]  41% with 0 failures
 Completed [=================================>-------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  42% with 0 failures
 Completed [==================================>------------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  43% with 0 failures
 Completed [===================================>-----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  44% with 0 failures
 Completed [====================================>----------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  45% with 0 failures
 Completed [=====================================>---------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  46% with 0 failures
 Completed [======================================>--------------------------------------------]  47% with 0 failures
 Completed [======================================>--------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  48% with 0 failures
 Completed [=======================================>-------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  49% with 0 failures
 Completed [========================================>------------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  50% with 0 failures
 Completed [=========================================>-----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  51% with 0 failures
 Completed [==========================================>----------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  52% with 0 failures
 Completed [===========================================>---------------------------------------]  53% with 0 failures
 Completed [===========================================>---------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  54% with 0 failures
 Completed [============================================>--------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  55% with 0 failures
 Completed [=============================================>-------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  56% with 0 failures
 Completed [==============================================>------------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  57% with 0 failures
 Completed [===============================================>-----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  58% with 0 failures
 Completed [================================================>----------------------------------]  59% with 0 failures
 Completed [================================================>----------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  60% with 0 failures
 Completed [=================================================>---------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  61% with 0 failures
 Completed [==================================================>--------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  62% with 0 failures
 Completed [===================================================>-------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  63% with 0 failures
 Completed [====================================================>------------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  64% with 0 failures
 Completed [=====================================================>-----------------------------]  65% with 0 failures
 Completed [=====================================================>-----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  66% with 0 failures
 Completed [======================================================>----------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  67% with 0 failures
 Completed [=======================================================>---------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  68% with 0 failures
 Completed [========================================================>--------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  69% with 0 failures
 Completed [=========================================================>-------------------------]  70% with 0 failures
 Completed [==========================================================>------------------------]  71% with 0 failures
 Completed [==========================================================>------------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  72% with 0 failures
 Completed [===========================================================>-----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  73% with 0 failures
 Completed [============================================================>----------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  74% with 0 failures
 Completed [=============================================================>---------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  75% with 0 failures
 Completed [==============================================================>--------------------]  76% with 0 failures
 Completed [===============================================================>-------------------]  77% with 0 failures
 Completed [===============================================================>-------------------]  78% with 0 failures
 Completed [================================================================>------------------]  78% with 0 failures
 Completed [================================================================>------------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  79% with 0 failures
 Completed [=================================================================>-----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  80% with 0 failures
 Completed [==================================================================>----------------]  81% with 0 failures
 Completed [===================================================================>---------------]  81% with 0 failures
 Completed [===================================================================>---------------]  82% with 0 failures
 Completed [===================================================================>---------------]  83% with 0 failures
 Completed [====================================================================>--------------]  83% with 0 failures
 Completed [====================================================================>--------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  84% with 0 failures
 Completed [=====================================================================>-------------]  85% with 0 failures
 Completed [======================================================================>------------]  85% with 0 failures
 Completed [======================================================================>------------]  86% with 0 failures
 Completed [=======================================================================>-----------]  86% with 0 failures
 Completed [=======================================================================>-----------]  87% with 0 failures
 Completed [========================================================================>----------]  87% with 0 failures
 Completed [========================================================================>----------]  88% with 0 failures
 Completed [========================================================================>----------]  89% with 0 failures
 Completed [=========================================================================>---------]  89% with 0 failures
 Completed [=========================================================================>---------]  90% with 0 failures
 Completed [==========================================================================>--------]  90% with 0 failures
 Completed [==========================================================================>--------]  91% with 0 failures
 Completed [===========================================================================>-------]  91% with 0 failures
 Completed [===========================================================================>-------]  92% with 0 failures
 Completed [============================================================================>------]  92% with 0 failures
 Completed [============================================================================>------]  93% with 0 failures
 Completed [=============================================================================>-----]  93% with 0 failures
 Completed [=============================================================================>-----]  94% with 0 failures
 Completed [=============================================================================>-----]  95% with 0 failures
 Completed [==============================================================================>----]  95% with 0 failures
 Completed [==============================================================================>----]  96% with 0 failures
 Completed [===============================================================================>---]  96% with 0 failures
 Completed [===============================================================================>---]  97% with 0 failures
 Completed [================================================================================>--]  97% with 0 failures
 Completed [================================================================================>--]  98% with 0 failures
 Completed [=================================================================================>-]  98% with 0 failures
 Completed [=================================================================================>-]  99% with 0 failures
 Completed [==================================================================================>]  99% with 0 failures
 Completed [==================================================================================>] 100% with 0 failures
 Completed [===================================================================================] 100% with 0 failures
                                                                                                                     

Done!

top markers for the clusters of all of the cells and violin plots of their expression

top_markers = markers %>%
    group_by(cluster) %>%
    slice_max(n = 2, order_by = avg_log2FC)
VlnPlot(seurat.obj, features = c("Rbp1", "Dhrs3"))

VlnPlot(seurat.obj, features = c("Fstl1", "Bgn"))

VlnPlot(seurat.obj, features = c("Serpinh1", "Dsp"))

VlnPlot(seurat.obj, features = c("Prc1", "Birc5"))

categorizing the cells based off their cell cycle analysis

## cell cycle 
s.genes <- str_to_title(cc.genes$s.genes)
g2m.genes <- str_to_title(cc.genes$g2m.genes)

seurat.obj = CellCycleScoring(seurat.obj, s.features = s.genes, g2m.features = g2m.genes)
seurat.obj@meta.data$cat_cluster = cell_categorized$stage

plotting the comparison of the cell cycle results

clusters = DimPlot(seurat.obj, group.by = "RNA_snn_res.1.75", label = TRUE, reduction = "umap")
real_condition = DimPlot(seurat.obj, group.by = "cc_paper", label = TRUE, reduction = "umap") 
phase = DimPlot(seurat.obj, group.by = "Phase", label = TRUE, reduction = "umap") 
cat = DimPlot(seurat.obj, group.by = "cc_hclust", label = TRUE, reduction = "umap")

clusters|real_condition|cat|phase

NA
NA

subsetting the cells that fit with hclust and performing clustering on each group

#cca_seurat = subset(x = seurat.obj, subset = cc_hclust == "CCA")
#cci_seurat = subset(x = seurat.obj, subset = cc_hclust == "CCI")
cca_seurat = subset(x = seurat.obj, subset = Phase == "S" | Phase == "G2M")
cci_seurat = subset(x = seurat.obj, subset = Phase == "G1")

clustering CCI cels

cci_seurat = FindNeighbors(cci_seurat, dims = 1:15)
Computing nearest neighbor graph
Computing SNN
cci_seurat = FindClusters(cci_seurat, resolution = 1)
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 319
Number of edges: 12257

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5331
Number of communities: 4
Elapsed time: 0 seconds
cl= DimPlot(cci_seurat, group.by = "RNA_snn_res.1",label = TRUE)
pap = DimPlot(cci_seurat, group.by = "cat_paper", label = TRUE)
hgc = DimPlot(cci_seurat, group.by = "cat_cluster", label = TRUE)

cl|pap|hgc

identifying CCI cells

cci_markers = FindAllMarkers(cci_seurat, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
Calculating cluster 0

 Completed [=>------------------------------------------------------]   4% with 0 failures
 Completed [==>-----------------------------------------------------]   5% with 0 failures
 Completed [==>-----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [========================>-------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [==>-----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [========================>-------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Calculating cluster 1

 Completed [=>------------------------------------------------------]   3% with 0 failures
 Completed [=>------------------------------------------------------]   4% with 0 failures
 Completed [==>-----------------------------------------------------]   5% with 0 failures
 Completed [==>-----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [==========>---------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [========================>-------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [======================================>-----------------]  71% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [=>------------------------------------------------------]   3% with 0 failures
 Completed [=>------------------------------------------------------]   4% with 0 failures
 Completed [==>-----------------------------------------------------]   5% with 0 failures
 Completed [==>-----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [==========>---------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [========================>-------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [======================================>-----------------]  71% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Calculating cluster 2

 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [====================================================>---]  96% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [====================================================>---]  96% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Calculating cluster 3

 Completed [==>-----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [========================>-------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [====================================================>---]  96% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [==>-----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [========================>-------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [====================================================>---]  96% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
cci_top_markers = cci_markers %>%
    group_by(cluster) %>%
    slice_min(n = 5, order_by = p_val_adj)
VlnPlot(cci_seurat, features = c("Fstl1", "Bgn"), cols = c("purple", "light green", "red", "blue"))

VlnPlot(cci_seurat, features = c("Tnni3", "Smpx"), cols = c("purple", "light green", "red", "blue"))

VlnPlot(cci_seurat, features = c("Vcam1", "Tm4sf1"), cols = c("purple", "light green", "red", "blue"))

VlnPlot(cci_seurat, features = c("Clca2", "Cd200"), cols = c("purple", "light green", "red", "blue"))

VlnPlot(cci_seurat, features = c("Lox", "Tm4sf1"), cols = c("purple", "light green", "red", "blue"))

Fstl1 involved in endothelial cell differentiation and endothelial cell migration and Bgn is a gene that is used for connective tissue metabolism -> lower expression -> cluster 1 = iCM, cluster 2 likely pICM

Tnni3, smpx, dsp used for cardiomycoytes -> cluster 2 = pre-iCM, cluster 1 and 3 are still fibroblasts

Idents(cci_seurat)  = "RNA_snn_res.1"
cci_seurat = RenameIdents(cci_seurat, `0` = "0")
cci_seurat = RenameIdents(cci_seurat, `1` = "iCM")
cci_seurat = RenameIdents(cci_seurat, `2` = "piCM")
cci_seurat = RenameIdents(cci_seurat, `3` = "3")
cl= DimPlot(cci_seurat, label = TRUE, cols = c("purple", "light green", "red", "blue"))
pap = DimPlot(cci_seurat, group.by = "cat_paper", label = TRUE, cols = c("blue", "red", "purple", "light green"))
hgc = DimPlot(cci_seurat, group.by = "cat_cluster", label = TRUE, cols = c("blue", "red", "purple", "light green"))

cl|pap|hgc

clustering CCA cells

cca_seurat = FindNeighbors(cca_seurat, dims = 1:15)
Computing nearest neighbor graph
Computing SNN
cca_seurat = FindClusters(cca_seurat, resolution = 1)
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 135
Number of edges: 4159

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.4323
Number of communities: 4
Elapsed time: 0 seconds
cl= DimPlot(cca_seurat, group.by = "RNA_snn_res.1",label = TRUE)
pap = DimPlot(cca_seurat, group.by = "cat_paper", label = TRUE)
cl|pap

identifying CCA cells

cca_markers = FindAllMarkers(cca_seurat, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
Calculating cluster 0

 Completed [==>-----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [========================>-------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [======================================>-----------------]  71% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [========================>-------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [======================================>-----------------]  71% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Calculating cluster 1

 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [==========>---------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [==========>---------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Calculating cluster 2

 Completed [=>------------------------------------------------------]   4% with 0 failures
 Completed [==>-----------------------------------------------------]   4% with 0 failures
 Completed [==>-----------------------------------------------------]   5% with 0 failures
 Completed [==>-----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [==========>---------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [========================>-------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [======================================>-----------------]  71% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [====================================================>---]  96% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [=>------------------------------------------------------]   4% with 0 failures
 Completed [==>-----------------------------------------------------]   4% with 0 failures
 Completed [==>-----------------------------------------------------]   5% with 0 failures
 Completed [==>-----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [==========>---------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [========================>-------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [======================================>-----------------]  71% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [====================================================>---]  96% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Calculating cluster 3

 Completed [=>------------------------------------------------------]   4% with 0 failures
 Completed [==>-----------------------------------------------------]   4% with 0 failures
 Completed [==>-----------------------------------------------------]   5% with 0 failures
 Completed [==>-----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [==========>---------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [======================================>-----------------]  71% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [====================================================>---]  96% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [==>-----------------------------------------------------]   5% with 0 failures
 Completed [==>-----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   6% with 0 failures
 Completed [===>----------------------------------------------------]   7% with 0 failures
 Completed [===>----------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   8% with 0 failures
 Completed [====>---------------------------------------------------]   9% with 0 failures
 Completed [====>---------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  10% with 0 failures
 Completed [=====>--------------------------------------------------]  11% with 0 failures
 Completed [=====>--------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  12% with 0 failures
 Completed [======>-------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  13% with 0 failures
 Completed [=======>------------------------------------------------]  14% with 0 failures
 Completed [=======>------------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  15% with 0 failures
 Completed [========>-----------------------------------------------]  16% with 0 failures
 Completed [========>-----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  17% with 0 failures
 Completed [=========>----------------------------------------------]  18% with 0 failures
 Completed [=========>----------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  19% with 0 failures
 Completed [==========>---------------------------------------------]  20% with 0 failures
 Completed [==========>---------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  21% with 0 failures
 Completed [===========>--------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  22% with 0 failures
 Completed [============>-------------------------------------------]  23% with 0 failures
 Completed [============>-------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  24% with 0 failures
 Completed [=============>------------------------------------------]  25% with 0 failures
 Completed [=============>------------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  26% with 0 failures
 Completed [==============>-----------------------------------------]  27% with 0 failures
 Completed [==============>-----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  28% with 0 failures
 Completed [===============>----------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  29% with 0 failures
 Completed [================>---------------------------------------]  30% with 0 failures
 Completed [================>---------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  31% with 0 failures
 Completed [=================>--------------------------------------]  32% with 0 failures
 Completed [=================>--------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  33% with 0 failures
 Completed [==================>-------------------------------------]  34% with 0 failures
 Completed [==================>-------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  35% with 0 failures
 Completed [===================>------------------------------------]  36% with 0 failures
 Completed [===================>------------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  37% with 0 failures
 Completed [====================>-----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  38% with 0 failures
 Completed [=====================>----------------------------------]  39% with 0 failures
 Completed [=====================>----------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  40% with 0 failures
 Completed [======================>---------------------------------]  41% with 0 failures
 Completed [======================>---------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  42% with 0 failures
 Completed [=======================>--------------------------------]  43% with 0 failures
 Completed [=======================>--------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  44% with 0 failures
 Completed [========================>-------------------------------]  45% with 0 failures
 Completed [=========================>------------------------------]  46% with 0 failures
 Completed [=========================>------------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  47% with 0 failures
 Completed [==========================>-----------------------------]  48% with 0 failures
 Completed [==========================>-----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  49% with 0 failures
 Completed [===========================>----------------------------]  50% with 0 failures
 Completed [===========================>----------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  51% with 0 failures
 Completed [============================>---------------------------]  52% with 0 failures
 Completed [============================>---------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  53% with 0 failures
 Completed [=============================>--------------------------]  54% with 0 failures
 Completed [==============================>-------------------------]  55% with 0 failures
 Completed [==============================>-------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  56% with 0 failures
 Completed [===============================>------------------------]  57% with 0 failures
 Completed [===============================>------------------------]  58% with 0 failures
 Completed [================================>-----------------------]  58% with 0 failures
 Completed [================================>-----------------------]  59% with 0 failures
 Completed [================================>-----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  60% with 0 failures
 Completed [=================================>----------------------]  61% with 0 failures
 Completed [=================================>----------------------]  62% with 0 failures
 Completed [==================================>---------------------]  62% with 0 failures
 Completed [==================================>---------------------]  63% with 0 failures
 Completed [===================================>--------------------]  63% with 0 failures
 Completed [===================================>--------------------]  64% with 0 failures
 Completed [===================================>--------------------]  65% with 0 failures
 Completed [====================================>-------------------]  65% with 0 failures
 Completed [====================================>-------------------]  66% with 0 failures
 Completed [====================================>-------------------]  67% with 0 failures
 Completed [=====================================>------------------]  67% with 0 failures
 Completed [=====================================>------------------]  68% with 0 failures
 Completed [=====================================>------------------]  69% with 0 failures
 Completed [======================================>-----------------]  69% with 0 failures
 Completed [======================================>-----------------]  70% with 0 failures
 Completed [======================================>-----------------]  71% with 0 failures
 Completed [=======================================>----------------]  71% with 0 failures
 Completed [=======================================>----------------]  72% with 0 failures
 Completed [========================================>---------------]  72% with 0 failures
 Completed [========================================>---------------]  73% with 0 failures
 Completed [========================================>---------------]  74% with 0 failures
 Completed [=========================================>--------------]  74% with 0 failures
 Completed [=========================================>--------------]  75% with 0 failures
 Completed [=========================================>--------------]  76% with 0 failures
 Completed [==========================================>-------------]  76% with 0 failures
 Completed [==========================================>-------------]  77% with 0 failures
 Completed [==========================================>-------------]  78% with 0 failures
 Completed [===========================================>------------]  78% with 0 failures
 Completed [===========================================>------------]  79% with 0 failures
 Completed [============================================>-----------]  79% with 0 failures
 Completed [============================================>-----------]  80% with 0 failures
 Completed [============================================>-----------]  81% with 0 failures
 Completed [=============================================>----------]  81% with 0 failures
 Completed [=============================================>----------]  82% with 0 failures
 Completed [=============================================>----------]  83% with 0 failures
 Completed [==============================================>---------]  83% with 0 failures
 Completed [==============================================>---------]  84% with 0 failures
 Completed [==============================================>---------]  85% with 0 failures
 Completed [===============================================>--------]  85% with 0 failures
 Completed [===============================================>--------]  86% with 0 failures
 Completed [===============================================>--------]  87% with 0 failures
 Completed [================================================>-------]  87% with 0 failures
 Completed [================================================>-------]  88% with 0 failures
 Completed [=================================================>------]  88% with 0 failures
 Completed [=================================================>------]  89% with 0 failures
 Completed [=================================================>------]  90% with 0 failures
 Completed [==================================================>-----]  90% with 0 failures
 Completed [==================================================>-----]  91% with 0 failures
 Completed [==================================================>-----]  92% with 0 failures
 Completed [===================================================>----]  92% with 0 failures
 Completed [===================================================>----]  93% with 0 failures
 Completed [===================================================>----]  94% with 0 failures
 Completed [====================================================>---]  94% with 0 failures
 Completed [====================================================>---]  95% with 0 failures
 Completed [====================================================>---]  96% with 0 failures
 Completed [=====================================================>--]  96% with 0 failures
 Completed [=====================================================>--]  97% with 0 failures
 Completed [======================================================>-]  97% with 0 failures
 Completed [======================================================>-]  98% with 0 failures
 Completed [======================================================>-]  99% with 0 failures
 Completed [=======================================================>]  99% with 0 failures
 Completed [=======================================================>] 100% with 0 failures
 Completed [========================================================] 100% with 0 failures
                                                                                          

Done!
cca_top_markers = cca_markers %>%
    group_by(cluster) %>%
    slice_min(n = 5, order_by = p_val_adj)

VlnPlot(cca_seurat, features = c("Fstl1", "Bgn"), cols = c("blue", "purple", "light green", "red"))

VlnPlot(cca_seurat, features = c("Tnni3", "Smpx"), cols = c("blue", "purple", "light green", "red"))

VlnPlot(cca_seurat, features = c("Vcam1", "Tm4sf1"), cols = c("blue", "purple", "light green", "red"))

VlnPlot(cca_seurat, features = c("Clca2", "Cd200"), cols = c("blue", "purple", "light green", "red"))

NA
NA

Tnni3 related to heart fucntion -> iCM= 2

Idents(cca_seurat)  = "RNA_snn_res.1"
cca_seurat = RenameIdents(cca_seurat, `2` = "iCM")
cca_seurat = RenameIdents(cca_seurat, `1` = "1")
cca_seurat = RenameIdents(cca_seurat, `0` = "0")
cca_seurat = RenameIdents(cca_seurat, `3` = "3")
cl= DimPlot(cca_seurat, label = TRUE,cols = c("blue", "purple", "light green", "red"))
pap = DimPlot(cca_seurat, group.by = "cat_paper", label = TRUE, cols = c("blue", "red", "purple", "light green"))
hgc = DimPlot(cca_seurat, group.by = "cat_cluster", label = TRUE, cols = c("blue", "red", "purple", "light green"))
cl|pap|hgc

Trying out SCTransform which is supposedly better for single cell data

seurat.sc = CreateSeuratObject(counts = exp)
seurat.sc = SCTransform(seurat.sc)
Calculating cell attributes from input UMI matrix: log_umi
Variance stabilizing transformation of count matrix of size 14028 by 454
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 2000 genes, 454 cells

  |                                                                                        
  |                                                                                  |   0%
  |                                                                                        
  |====================                                                              |  25%
  |                                                                                        
  |=========================================                                         |  50%
  |                                                                                        
  |==============================================================                    |  75%
  |                                                                                        
  |==================================================================================| 100%
Second step: Get residuals using fitted parameters for 14028 genes

  |                                                                                        
  |                                                                                  |   0%
  |                                                                                        
  |===                                                                               |   3%
  |                                                                                        
  |======                                                                            |   7%
  |                                                                                        
  |========                                                                          |  10%
  |                                                                                        
  |===========                                                                       |  14%
  |                                                                                        
  |==============                                                                    |  17%
  |                                                                                        
  |=================                                                                 |  21%
  |                                                                                        
  |====================                                                              |  24%
  |                                                                                        
  |=======================                                                           |  28%
  |                                                                                        
  |=========================                                                         |  31%
  |                                                                                        
  |============================                                                      |  34%
  |                                                                                        
  |===============================                                                   |  38%
  |                                                                                        
  |==================================                                                |  41%
  |                                                                                        
  |=====================================                                             |  45%
  |                                                                                        
  |========================================                                          |  48%
  |                                                                                        
  |==========================================                                        |  52%
  |                                                                                        
  |=============================================                                     |  55%
  |                                                                                        
  |================================================                                  |  59%
  |                                                                                        
  |===================================================                               |  62%
  |                                                                                        
  |======================================================                            |  66%
  |                                                                                        
  |=========================================================                         |  69%
  |                                                                                        
  |===========================================================                       |  72%
  |                                                                                        
  |==============================================================                    |  76%
  |                                                                                        
  |=================================================================                 |  79%
  |                                                                                        
  |====================================================================              |  83%
  |                                                                                        
  |=======================================================================           |  86%
  |                                                                                        
  |==========================================================================        |  90%
  |                                                                                        
  |============================================================================      |  93%
  |                                                                                        
  |===============================================================================   |  97%
  |                                                                                        
  |==================================================================================| 100%
Computing corrected count matrix for 14028 genes

  |                                                                                        
  |                                                                                  |   0%
  |                                                                                        
  |===                                                                               |   3%
  |                                                                                        
  |======                                                                            |   7%
  |                                                                                        
  |========                                                                          |  10%
  |                                                                                        
  |===========                                                                       |  14%
  |                                                                                        
  |==============                                                                    |  17%
  |                                                                                        
  |=================                                                                 |  21%
  |                                                                                        
  |====================                                                              |  24%
  |                                                                                        
  |=======================                                                           |  28%
  |                                                                                        
  |=========================                                                         |  31%
  |                                                                                        
  |============================                                                      |  34%
  |                                                                                        
  |===============================                                                   |  38%
  |                                                                                        
  |==================================                                                |  41%
  |                                                                                        
  |=====================================                                             |  45%
  |                                                                                        
  |========================================                                          |  48%
  |                                                                                        
  |==========================================                                        |  52%
  |                                                                                        
  |=============================================                                     |  55%
  |                                                                                        
  |================================================                                  |  59%
  |                                                                                        
  |===================================================                               |  62%
  |                                                                                        
  |======================================================                            |  66%
  |                                                                                        
  |=========================================================                         |  69%
  |                                                                                        
  |===========================================================                       |  72%
  |                                                                                        
  |==============================================================                    |  76%
  |                                                                                        
  |=================================================================                 |  79%
  |                                                                                        
  |====================================================================              |  83%
  |                                                                                        
  |=======================================================================           |  86%
  |                                                                                        
  |==========================================================================        |  90%
  |                                                                                        
  |============================================================================      |  93%
  |                                                                                        
  |===============================================================================   |  97%
  |                                                                                        
  |==================================================================================| 100%
Calculating gene attributes
Wall clock passed: Time difference of 6.438817 secs
Determine variable features
Place corrected count matrix in counts slot
Centering data matrix

  |                                                                                        
  |                                                                                  |   0%
  |                                                                                        
  |====================                                                              |  25%
  |                                                                                        
  |=========================================                                         |  50%
  |                                                                                        
  |==============================================================                    |  75%
  |                                                                                        
  |==================================================================================| 100%
Set default assay to SCT
seurat.sc = RunPCA(seurat.sc, features =  VariableFeatures(seurat.sc))
PC_ 1 
Positive:  Bgn, Fstl1, Postn, Col1a2, Cd200, Col3a1, Rbp1, Tagln, Dhrs3, Tagln2 
       Acta2, 11-Sep, Fbln2, Clca1, Lox, Wisp2, Col8a1, Anxa1, Fam198b, Marcks 
       Ogn, Col5a2, Fbn1, Pdpn, Asns, Adamts5, Acot2, Irgm1, Tcf21, Ptprb 
Negative:  Tnnt2, Nid2, Acaa2, Myl4, Ldhb, Dsp, Ehd4, Clu, Tnni3, Smpx 
       Ttn, Ryr2, Myl7, Cd24a, Gpx3, Epb4.1, Fam134b, Ppp1r3c, Sort1, Mgrn1 
       Mlf1, Rn45s, Ldb3, Cenpa, Rrad, Fabp3, Arhgap44, Mgst3, Lgals3, Ptrf 
PC_ 2 
Positive:  Top2a, Smc2, Ccnb1, Cdk1, Prc1, Mki67, Rrm2, H2afz, Stmn1, Tpx2 
       Cdca8, Anln, Pbk, Birc5, Tacc3, Ckap2l, Asf1b, Mad2l1, Hmgn2, Hmmr 
       Ube2c, Rrm1, Cenpe, Kif20b, Cks2, Ndc80, Shcbp1, Spc25, Hmgb2, Cdca3 
Negative:  Cst3, Gyg, Malat1, Gpx3, Sptbn1, B2m, Ogn, Fhl2, Sparc, Dhrs3 
       Serpine2, Tnnt2, Impact, Rbp1, Col5a2, Sat1, Fn1, Itgb5, B4galt1, Col4a2 
       Serpina3h, Lama2, Tmsb4x, Postn, Gucy1a3, Adamtsl2, Hsd11b1, Adamts5, Ttyh2, Myl9 
PC_ 3 
Positive:  Mgst1, Pdpn, Vcam1, Ftl1, F11r, Efna5, Cyp1b1, Sdc4, Ptgs1, Gpm6a 
       Steap1, Ezr, Upk1b, Ctsl, Dcn, Ccl2, Gsta4, Maf, Flrt2, Msln 
       Efemp1, Timp3, Igfbp4, Cxadr, Hpgd, Dpp4, Gja1, Mpzl2, F3, Bnc1 
Negative:  Myl9, Ankrd1, Acta2, Cst3, Sorbs2, Tnnt2, Fhl2, Mustn1, Tmsb4x, Flna 
       Pdlim3, Lmcd1, Tagln, Col4a1, Pls3, Lpp, Postn, Wisp2, Gyg, Gpx3 
       Sh3bgrl, Myl4, Col4a2, Itga8, Pdlim2, Fn1, Nid2, Vim, Myom1, Csrp2 
PC_ 4 
Positive:  Tpm1, Acta2, Tagln, Anxa1, Actg1, Actb, Cav1, Anxa2, Myl9, Tmsb4x 
       Prss23, Efemp1, Cryab, Mustn1, Zyx, Flna, Arl5a, Lox, S100a4, Col8a1 
       Spcs3, Thbs1, Pls3, Fhl1, Ccnd2, Upk1b, Lpp, Map6, Plec, Ankrd1 
Negative:  Dcn, Abcg1, Rbp1, B2m, Igf2r, Hsd11b1, Gpx3, B4galt1, Mmp2, Mgp 
       Serpine2, Cxcl1, Serpina3g, Cp, Angptl2, Ttyh2, Serpina3h, Rab31, Ccl7, Serpina3n 
       Tmem176b, Srpx2, Gpm6b, Sepp1, Ctsl, Btg2, Ccl2, Btg1, Dhrs3, Casp4 
PC_ 5 
Positive:  Serpina3h, Col1a2, Col1a1, Serpina3i, Col4a1, Lsp1, Csf1, Ch25h, Asns, Des 
       Ccl7, Wisp1, Col6a3, Adamtsl2, Gfpt2, Lgals1, Timp1, Serpina3g, Psat1, Ankrd1 
       Col4a2, Nars, Flnb, Pcolce, Postn, Chst11, Ccnd1, Ckb, Rn45s, Flna 
Negative:  Spcs3, Sptbn1, Btg1, Impact, Phactr2, Akap13, Rab31, Cd93, Cfh, Slc38a2 
       Myo10, Arl5a, Sh3bgrl, Adamts5, Ddah1, Tspan12, Fryl, Gucy1a3, Lmcd1, Canx 
       Id3, Adamtsl3, Prss23, Eln, Clca1, B230120H23Rik, 5430417L22Rik, Wisp2, AI597468, Fn1 
identified_cells = identified_cells[match(rownames(seurat.sc@meta.data), rownames(identified_cells)),]
seurat.sc@meta.data$cc_paper = identified_cells$CC
seurat.sc@meta.data$cat_paper = identified_cells$stage

seurat.sc = RunUMAP(seurat.sc, dims = 1:15)
Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session
12:32:25 UMAP embedding parameters a = 0.9922 b = 1.112
12:32:25 Read 454 rows and found 15 numeric columns
12:32:25 Using Annoy for neighbor search, n_neighbors = 30
12:32:25 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
12:32:25 Writing NN index file to temp file /var/folders/fj/09brpj8s5mz1c5wxktl80s080000gn/T//Rtmp8VGprm/file153ed68dea2d5
12:32:25 Searching Annoy index using 1 thread, search_k = 3000
12:32:25 Annoy recall = 100%
12:32:25 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
12:32:26 Initializing from normalized Laplacian + noise (using irlba)
12:32:26 Commencing optimization for 500 epochs, with 17490 positive edges
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
12:32:27 Optimization finished
seurat.sc = FindNeighbors(seurat.sc, dims = 1:15)
Computing nearest neighbor graph
Computing SNN
seurat.sc = FindClusters(seurat.sc, resolution = 1.75)
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 454
Number of edges: 15941

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.4966
Number of communities: 8
Elapsed time: 0 seconds
seurat.sc = CellCycleScoring(seurat.sc, s.features = s.genes, g2m.features = g2m.genes)
clusters = DimPlot(seurat.sc, group.by = "SCT_snn_res.1.75", label = TRUE, reduction = "umap")
real_condition = DimPlot(seurat.sc, group.by = "cc_paper", label = TRUE, reduction = "umap") 
phase = DimPlot(seurat.sc, group.by = "Phase", label = TRUE, reduction = "umap") 
cat = DimPlot(seurat.sc, group.by = "cat_paper", label = TRUE, reduction = "umap") 

clusters|real_condition|phase|cat

The results are largely the same so just going to continue on with the original clsutering.

---
title: "Seurat Cell Categorization"
author: "Reha Mathur"
output: html_notebook
---
## importing packages 
```{r}
library("devtools")
install_github("jw156605/SLICER")
library(Seurat)
library(readr)
library(tidyverse)
library(HGC) 
library(latticeExtra)
library(lattice) 
library(RColorBrewer)
library(clusterProfiler)
library(org.Mm.eg.db)
library(AnnotationDbi)
```
## reading in normalized data again
```{r}
exp = read_csv("normalized_data.csv")
exp = discard(exp,~all(is.na(.) |.  == ""))
exp = distinct(exp, `...1`, .keep_all = TRUE)
# filtering out the reprogramming transcription factors 
exp = filter(exp, !`...1`%in% c("Mef2c", "Gata4", "Tbx5"))
exp = column_to_rownames(exp, var="...1")

```
## creating a seurat object with all of the cells 

```{r}
seurat.obj = CreateSeuratObject(counts = exp)
```
```{r}
# using seurat to noramlize, scale and dimensionally reduce the data 
seurat.obj = NormalizeData(seurat.obj)
seurat.obj = FindVariableFeatures(seurat.obj, selection.method =  "vst", nfeatures = 10000)
all.genes = rownames(seurat.obj)
seurat.obj = ScaleData(seurat.obj, features = all.genes)
seurat.obj = RunPCA(seurat.obj, features =  VariableFeatures(seurat.obj))

```
```{r}
# elbow plot to see the correct number of dimensions
ElbowPlot(seurat.obj)
```
## Seurat clustering the entire graph to see what clusters are identified 
```{r}
seurat.obj = FindNeighbors(seurat.obj, dims = 1:15)
```

```{r}
seurat.obj = FindClusters(seurat.obj, resolution = 1.75)
```
## importing the results from the paper and our hierarchical clustering results for further comparison
```{r}
identified_cells = read.csv("paper_cell_states.csv", row.names = 1, header=TRUE)
```
```{r}
identified_cells = identified_cells[match(rownames(seurat.obj@meta.data), rownames(identified_cells)),]
seurat.obj@meta.data$cc_paper = identified_cells$CC
seurat.obj@meta.data$cat_paper = identified_cells$stage
seurat.obj@meta.data$cc_hclust = "CCI"
seurat.obj@meta.data[active_cells,]$cc_hclust = "CCA"

```


```{r}
Idents(seurat.obj)  = "RNA_snn_res.1.75"
```
## running UMAP dimensional reduction on the data to plot the data 
```{r}
seurat.obj = RunUMAP(seurat.obj, dims = 1:15)
```
# seeing what tsne reduction makes the data do 
```{r}
seurat.obj = RunTSNE(seurat.obj, dims = 1:15)
DimPlot(seurat.obj, reduction = "tsne", group.by = 'RNA_snn_res.1.75')
``` 
# finding differentially expressed markers in these clusters
```{r}
markers = FindAllMarkers(seurat.obj, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
```
# top markers for the clusters of all of the cells and violin plots of their expression 
```{r}
top_markers = markers %>%
    group_by(cluster) %>%
    slice_max(n = 2, order_by = avg_log2FC)
```

```{r}
VlnPlot(seurat.obj, features = c("Rbp1", "Dhrs3"))
VlnPlot(seurat.obj, features = c("Fstl1", "Bgn"))
VlnPlot(seurat.obj, features = c("Serpinh1", "Dsp"))
VlnPlot(seurat.obj, features = c("Prc1", "Birc5"))
```
## categorizing the cells based off their cell cycle analysis 
```{r}
## cell cycle 
s.genes <- str_to_title(cc.genes$s.genes)
g2m.genes <- str_to_title(cc.genes$g2m.genes)

seurat.obj = CellCycleScoring(seurat.obj, s.features = s.genes, g2m.features = g2m.genes)
seurat.obj@meta.data$cat_cluster = cell_categorized$stage

```

## plotting the comparison of the cell cycle results
```{r}
clusters = DimPlot(seurat.obj, group.by = "RNA_snn_res.1.75", label = TRUE, reduction = "umap")
real_condition = DimPlot(seurat.obj, group.by = "cc_paper", label = TRUE, reduction = "umap") 
phase = DimPlot(seurat.obj, group.by = "Phase", label = TRUE, reduction = "umap") 
cat = DimPlot(seurat.obj, group.by = "cc_hclust", label = TRUE, reduction = "umap")

clusters|real_condition|cat|phase


```



## subsetting the cells that fit with hclust and performing clustering on each group 

```{r}
#cca_seurat = subset(x = seurat.obj, subset = cc_hclust == "CCA")
#cci_seurat = subset(x = seurat.obj, subset = cc_hclust == "CCI")
cca_seurat = subset(x = seurat.obj, subset = Phase == "S" | Phase == "G2M")
cci_seurat = subset(x = seurat.obj, subset = Phase == "G1")
```

## clustering CCI cels 

```{r}
cci_seurat = FindNeighbors(cci_seurat, dims = 1:15)
cci_seurat = FindClusters(cci_seurat, resolution = 1)
```

```{r}
cl= DimPlot(cci_seurat, group.by = "RNA_snn_res.1",label = TRUE)
pap = DimPlot(cci_seurat, group.by = "cat_paper", label = TRUE)
hgc = DimPlot(cci_seurat, group.by = "cat_cluster", label = TRUE)

cl|pap|hgc
```
## identifying CCI cells 

```{r}
cci_markers = FindAllMarkers(cci_seurat, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
```
```{r}
cci_top_markers = cci_markers %>%
    group_by(cluster) %>%
    slice_min(n = 5, order_by = p_val_adj)
```

```{r}
VlnPlot(cci_seurat, features = c("Fstl1", "Bgn"), cols = c("purple", "light green", "red", "blue"))
VlnPlot(cci_seurat, features = c("Tnni3", "Smpx"), cols = c("purple", "light green", "red", "blue"))
VlnPlot(cci_seurat, features = c("Vcam1", "Tm4sf1"), cols = c("purple", "light green", "red", "blue"))
VlnPlot(cci_seurat, features = c("Clca2", "Cd200"), cols = c("purple", "light green", "red", "blue"))
VlnPlot(cci_seurat, features = c("Lox", "Tm4sf1"), cols = c("purple", "light green", "red", "blue"))

```

Fstl1 involved in endothelial cell differentiation and endothelial cell migration and Bgn is a gene that is used for connective tissue metabolism -> lower expression -> cluster 1 = iCM, cluster 2 likely pICM

Tnni3, smpx, dsp used for cardiomycoytes -> cluster 2 = pre-iCM, cluster 1 and 3 are still fibroblasts 

```{r}
Idents(cci_seurat)  = "RNA_snn_res.1"
cci_seurat = RenameIdents(cci_seurat, `0` = "0")
cci_seurat = RenameIdents(cci_seurat, `1` = "iCM")
cci_seurat = RenameIdents(cci_seurat, `2` = "piCM")
cci_seurat = RenameIdents(cci_seurat, `3` = "3")

```

```{r}
cl= DimPlot(cci_seurat, label = TRUE, cols = c("purple", "light green", "red", "blue"))
pap = DimPlot(cci_seurat, group.by = "cat_paper", label = TRUE, cols = c("blue", "red", "purple", "light green"))
hgc = DimPlot(cci_seurat, group.by = "cat_cluster", label = TRUE, cols = c("blue", "red", "purple", "light green"))

cl|pap|hgc
```
## clustering CCA cells

```{r}
cca_seurat = FindNeighbors(cca_seurat, dims = 1:15)
cca_seurat = FindClusters(cca_seurat, resolution = 1)
```

```{r}
cl= DimPlot(cca_seurat, group.by = "RNA_snn_res.1",label = TRUE)
pap = DimPlot(cca_seurat, group.by = "cat_paper", label = TRUE)
cl|pap
```
## identifying CCA cells 

```{r}
cca_markers = FindAllMarkers(cca_seurat, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
```
```{r}
cca_top_markers = cca_markers %>%
    group_by(cluster) %>%
    slice_min(n = 5, order_by = p_val_adj)
```

```{r}
VlnPlot(cca_seurat, features = c("Fstl1", "Bgn"), cols = c("blue", "purple", "light green", "red"))
VlnPlot(cca_seurat, features = c("Tnni3", "Smpx"), cols = c("blue", "purple", "light green", "red"))
VlnPlot(cca_seurat, features = c("Vcam1", "Tm4sf1"), cols = c("blue", "purple", "light green", "red"))
VlnPlot(cca_seurat, features = c("Clca2", "Cd200"), cols = c("blue", "purple", "light green", "red"))
```
#### 

Tnni3 related to heart fucntion -> iCM= 2 

```{r}
Idents(cca_seurat)  = "RNA_snn_res.1"
cca_seurat = RenameIdents(cca_seurat, `2` = "iCM")
cca_seurat = RenameIdents(cca_seurat, `1` = "1")
cca_seurat = RenameIdents(cca_seurat, `0` = "0")
cca_seurat = RenameIdents(cca_seurat, `3` = "3")
```

```{r}
cl= DimPlot(cca_seurat, label = TRUE,cols = c("blue", "purple", "light green", "red"))
pap = DimPlot(cca_seurat, group.by = "cat_paper", label = TRUE, cols = c("blue", "red", "purple", "light green"))
hgc = DimPlot(cca_seurat, group.by = "cat_cluster", label = TRUE, cols = c("blue", "red", "purple", "light green"))
cl|pap|hgc

```

## Trying out SCTransform which is supposedly better for single cell data
```{r}
seurat.sc = CreateSeuratObject(counts = exp)
seurat.sc = SCTransform(seurat.sc)
```
```{r}
seurat.sc = RunPCA(seurat.sc, features =  VariableFeatures(seurat.sc))
```

```{r}
identified_cells = identified_cells[match(rownames(seurat.sc@meta.data), rownames(identified_cells)),]
seurat.sc@meta.data$cc_paper = identified_cells$CC
seurat.sc@meta.data$cat_paper = identified_cells$stage

seurat.sc = RunUMAP(seurat.sc, dims = 1:15)
seurat.sc = FindNeighbors(seurat.sc, dims = 1:15)
seurat.sc = FindClusters(seurat.sc, resolution = 1.75)
```

```{r}
seurat.sc = CellCycleScoring(seurat.sc, s.features = s.genes, g2m.features = g2m.genes)
```

```{r}
clusters = DimPlot(seurat.sc, group.by = "SCT_snn_res.1.75", label = TRUE, reduction = "umap")
real_condition = DimPlot(seurat.sc, group.by = "cc_paper", label = TRUE, reduction = "umap") 
phase = DimPlot(seurat.sc, group.by = "Phase", label = TRUE, reduction = "umap") 
cat = DimPlot(seurat.sc, group.by = "cat_paper", label = TRUE, reduction = "umap") 

clusters|real_condition|phase|cat

```

The results are largely the same so just going to continue on with the original clsutering. 